Application of Next-Generation Sequencing for Disease Diagnosis in the Beehive
New Review Highlights NGS as a Complementary Tool for Honey Bee Brood Disease Investigations
A review published in Frontiers in Bee Science examines how next-generation sequencing can support veterinarians and beekeepers investigating bacterial disease in managed honey bee (Apis mellifera) colonies.
Authored by Dr. Jörg Mayer of the University of Georgia College of Veterinary Medicine, the paper combines a review of targeted NGS in apiculture with four field cases involving abnormal brood patterns and suspected European foulbrood.
The clinical examples demonstrate how 16S rRNA gene amplicon sequencing can provide microbial evidence that complements visual inspection, colony history and established diagnostic methods.
Moving Beyond the Appearance of the Brood
Irregular, patchy or “shotgun” brood patterns may raise concern for European foulbrood, but appearance alone may not identify the underlying cause.
European foulbrood is primarily associated with Melissococcus plutonius, a fastidious bacterium that can be difficult to recover through culture. Its abundance may also decline after larval death while secondary organisms become more prominent, potentially complicating interpretation.
Targeted NGS offers a culture-independent approach. Rather than requiring organisms to remain viable through collection, transport, and laboratory growth, sequencing detects microbial DNA present in the submitted sample and characterizes the broader bacterial community.
Four Field Cases Demonstrate Different Diagnostic Applications
The paper presents four honey bee brood investigations:
- Longitudinal microbial monitoring: One colony was sampled repeatedly over several months. Sequencing initially found no M. plutonius, later detected it at a low level and subsequently documented a marked increase alongside the development of an abnormal brood pattern. Follow-up testing showed a substantial reduction, although the paper cautions that seasonality and other factors prevent attributing the change to a single intervention.
- Redirecting an EFB investigation: Another colony displayed brood abnormalities resembling European foulbrood, but sequencing did not detect bacterial pathogens consistent with EFB. Separate viral testing subsequently identified sacbrood virus, demonstrating how a negative bacterial finding can help redirect the diagnostic investigation.
- Characterizing secondary bacterial overgrowth: A third case detected M. plutonius alongside substantial Enterococcus faecalis. The findings were interpreted as European foulbrood with associated secondary bacterial overgrowth—not evidence that E. faecalis was necessarily the primary cause of disease.
- Documenting an unusual co-detection: The fourth case detected Paenibacillus dendritiformis together with M. plutonius. The author described this as the first documented detection of P. dendritiformis in honey bee colonies or larvae in the United States, while emphasizing that its pathogenic significance remains uncertain.
Together, these cases show that similar brood abnormalities can reflect different microbial findings and that detected organisms must be interpreted within the larger colony-health picture.
Supporting More Evidence-Based Antibiotic Decisions
Each case was submitted after a presumptive field diagnosis of European foulbrood and a request for antibiotic treatment. M. plutonius was detected in three of the four investigations. In the remaining case, the absence of bacterial findings consistent with EFB helped redirect the investigation toward a viral cause.
This distinction is important for antimicrobial stewardship. Molecular confirmation may help veterinarians determine when bacterial evidence supports an EFB diagnosis and when antibiotic treatment may not address the suspected cause.
MiDOG Testing in the Clinical Case Examples
MiDOG All-in-One Microbial Test reports are featured throughout the paper’s clinical cases. Larval samples were collected into a stabilization buffer and analyzed using a targeted NGS workflow combining bacterial 16S rRNA gene sequencing and fungal ITS sequencing.
This approach supports bacterial and fungal detection from the same submitted sample without relying on microbial growth in culture. In this paper, the primary diagnostic focus was the bacterial composition of honey bee larval samples.
NGS Results Still Require Clinical Context
The paper positions 16S rRNA gene sequencing as a complementary diagnostic tool, not a replacement for colony inspection, conventional testing, or veterinary interpretation.
As with other DNA-based methods, detection does not establish whether an organism is viable or confirm that it caused the observed disease. Relative abundance can also be influenced by sample selection, DNA extraction, amplification and the amount of microbial material present.
Results should therefore be considered alongside:
- Colony strength and queen status
- Clinical appearance of the brood
- Seasonality
- Varroa mite burden and management history
- Sample quality and collection methods
- Previous treatment and colony-health history
- Other bacterial, fungal, viral, or parasitic investigations
Advancing Veterinary Support for Honey Bee Health
Dr. Jörg Mayer is a professor of zoological medicine in the Department of Small Animal Medicine and Surgery at the University of Georgia College of Veterinary Medicine. His work includes honey bee colony health, veterinary involvement in apiculture, and the integration of emerging diagnostic technologies into exotic animal medicine.
The review reinforces the growing role veterinarians can play in honey bee health management and demonstrates how targeted NGS may add valuable microbial context when brood disease is suspected.
The publication was supported by the Georgia Beekeepers Association and the University of Georgia Foundation.
Read the Published Review
“Application of next-generation sequencing (NGS) for disease diagnosis in the beehive” was published in Frontiers in Bee Science on July 16, 2026.
Citation: Mayer J. (2026). Application of next-generation sequencing (NGS) for disease diagnosis in the beehive. Frontiers in Bee Science, 4:1862765. https://doi.org/10.3389/frbee.2026.1862765
